PDB-36zf: Crystal structure of a Phosphoribosylaminoimidazole carboxylase f...

ID or keywords:

Entry

Database: PDB / ID: 36zf

Title

Crystal structure of a Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (Apo, Orthorhombic P form)

Components

N5-carboxyaminoimidazole ribonucleotide synthase

Keywords

LYASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Phosphoribosylaminoimidazole carboxylase

Function / homology

Function and homology information

5-(carboxyamino)imidazole ribonucleotide synthase / 5-(carboxyamino)imidazole ribonucleotide synthase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Paraburkholderia xenovorans LB400 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: To be published
Title: Crystal structure of a Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (Apo, Orthorhombic P form)
Authors: Lanyi Lari, N. / Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Jul 7, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 15, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	36zf.cif.gz	607.2 KB	Display	PDBx/mmCIF format
PDB format	pdb36zf.ent.gz	500.9 KB	Display	PDB format
PDBx/mmJSON format	36zf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/6z/36zf ftp://data.pdbj.org/pub/pdb/validation_reports/6z/36zf	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (4) #192 - Dec 2015 Vancomycin similarity (4) #154 - Oct 2012 Citric Acid Cycle similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (4) #137 - May 2011 Cytochrome bc1 similarity (1)

Deposited unit

A: N5-carboxyaminoimidazole ribonucleotide synthase

B: N5-carboxyaminoimidazole ribonucleotide synthase

C: N5-carboxyaminoimidazole ribonucleotide synthase

D: N5-carboxyaminoimidazole ribonucleotide synthase

hetero molecules

170 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N5-carboxyaminoimidazole ribonucleotide synthase

B: N5-carboxyaminoimidazole ribonucleotide synthase

hetero molecules

defined by author&software
Evidence: gel filtration
85.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: N5-carboxyaminoimidazole ribonucleotide synthase

D: N5-carboxyaminoimidazole ribonucleotide synthase

hetero molecules

defined by author&software
85.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	101.621, 103.556, 151.285
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	N5-carboxyaminoimidazole ribonucleotide synthase / N5-CAIR synthase / 5-(carboxyamino)imidazole ribonucleotide synthetase Mass: 42509.523 Da / Num. of mol.: 4 / Fragment: S9-T397 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paraburkholderia xenovorans LB400 (bacteria) Gene: purK, Bxe_A0694 / Plasmid: BuxeA.00036.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q13UJ9, 5-(carboxyamino)imidazole ribonucleotide synthase
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 716 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.45 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200 mM NaF, 25% PEG 3350, BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. plate 20994 B6 drop 3, Puck: PSL-2513, Cryo: 20% ethylene glycol + 80% crystallant

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 13, 2026
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.05→48.99 Å / Num. obs: 100704 / % possible obs: 100 % / Redundancy: 13.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.123 / R_pim(I) all: 0.035 / R_rim(I) all: 0.128 / Net I/av σ(I): 1 / Net I/σ(I): 13.8
Reflection shell	Resolution: 2.05→2.09 Å / R_merge(I) obs: 1.635 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4956 / CC_1/2: 0.752 / R_pim(I) all: 0.458 / R_rim(I) all: 1.699 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(dev_6111: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.05→48.99 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2284	5133	5.1 %
R_work	0.1833	-	-
obs	0.1855	100613	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.05→48.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11539	0	21	716	12276

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	11954
X-RAY DIFFRACTION	f_angle_d	0.626	16314
X-RAY DIFFRACTION	f_dihedral_angle_d	15.088	4359
X-RAY DIFFRACTION	f_chiral_restr	0.047	1882
X-RAY DIFFRACTION	f_plane_restr	0.007	2167

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.05-2.07	0.2896	158	0.264	3225	X-RAY DIFFRACTION	100
2.07-2.1	0.2956	168	0.2462	3112	X-RAY DIFFRACTION	100
2.1-2.12	0.2789	178	0.2337	3127	X-RAY DIFFRACTION	100
2.12-2.15	0.2951	211	0.2236	3084	X-RAY DIFFRACTION	100
2.15-2.18	0.2595	183	0.2171	3146	X-RAY DIFFRACTION	100
2.18-2.21	0.2669	163	0.2062	3192	X-RAY DIFFRACTION	100
2.21-2.24	0.2632	172	0.2098	3129	X-RAY DIFFRACTION	100
2.24-2.27	0.259	186	0.2149	3103	X-RAY DIFFRACTION	100
2.27-2.31	0.2775	145	0.21	3207	X-RAY DIFFRACTION	100
2.31-2.35	0.2421	190	0.2028	3115	X-RAY DIFFRACTION	100
2.35-2.39	0.2812	155	0.2079	3162	X-RAY DIFFRACTION	100
2.39-2.43	0.2972	154	0.2095	3186	X-RAY DIFFRACTION	100
2.43-2.48	0.2707	184	0.203	3158	X-RAY DIFFRACTION	100
2.48-2.53	0.2737	162	0.198	3141	X-RAY DIFFRACTION	100
2.53-2.58	0.2193	163	0.186	3172	X-RAY DIFFRACTION	100
2.58-2.64	0.2361	176	0.1775	3159	X-RAY DIFFRACTION	100
2.64-2.71	0.2505	189	0.1811	3147	X-RAY DIFFRACTION	100
2.71-2.78	0.2397	153	0.1913	3180	X-RAY DIFFRACTION	100
2.78-2.86	0.2363	194	0.194	3152	X-RAY DIFFRACTION	100
2.86-2.96	0.2446	168	0.2045	3192	X-RAY DIFFRACTION	100
2.96-3.06	0.255	126	0.2004	3209	X-RAY DIFFRACTION	100
3.06-3.18	0.2468	169	0.1993	3185	X-RAY DIFFRACTION	100
3.18-3.33	0.2313	202	0.1935	3175	X-RAY DIFFRACTION	100
3.33-3.51	0.2145	158	0.183	3205	X-RAY DIFFRACTION	100
3.51-3.72	0.2336	157	0.1814	3224	X-RAY DIFFRACTION	100
3.72-4.01	0.2083	182	0.1732	3191	X-RAY DIFFRACTION	100
4.01-4.42	0.1992	171	0.1448	3246	X-RAY DIFFRACTION	100
4.42-5.05	0.1643	170	0.1362	3236	X-RAY DIFFRACTION	100
5.05-6.36	0.1982	176	0.1749	3285	X-RAY DIFFRACTION	100
6.37-48.99	0.22	170	0.1784	3435	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.1474	-0.7079	-0.9232	3.6082	0.3341	6.987	-0.2874	-0.3572	-0.438	0.4171	0.2254	0.7165	0.1476	-0.4377	0.0866	0.2863	0.1069	0.0924	0.3287	0.0931	0.3068	0.8977	-1.2452	-25.3681
2	4.5665	-0.9691	-0.6504	5.7523	-0.8773	3.5014	-0.1203	0.4146	-0.3462	0.2051	0.2967	1.2773	-0.1448	-1.1224	-0.1062	0.382	0.1499	0.0434	0.6607	0.0691	0.5802	-8.0897	6.0301	-30.4068
3	0.3733	-0.5765	0.5718	1.303	-2.1567	4.6509	0.0105	0.0907	-0.146	0.0157	0.0567	0.1709	-0.1873	-0.4683	-0.0721	0.4206	0.0354	-0.0485	0.392	-0.0304	0.3783	-0.9544	10.0439	-45.5589
4	4.5532	2.6605	0.9056	4.4074	2.662	3.0641	0.0939	0.3296	-0.2073	-0.3346	-0.2273	0.5933	0.2233	-0.2345	0.0675	0.536	0.0866	-0.1603	0.3596	-0.0595	0.4795	-5.7651	1.5839	-63.2234
5	1.904	-0.9165	0.9686	1.5174	-0.3561	1.9242	0.0973	0.3175	-0.1109	-0.303	-0.0436	0.1782	0.0073	0.0389	-0.0457	0.3168	-0.0112	-0.011	0.2132	-0.016	0.2137	8.59	0.2581	-51.6413
6	1.187	-0.7064	0.314	0.8706	-0.2405	1.7712	0.0884	0.0692	-0.2926	-0.1293	-0.0032	0.1895	0.2313	-0.1283	-0.0486	0.245	0.006	-0.0351	0.1673	-0.0289	0.2401	11.0074	-13.6302	-37.6952
7	7.7543	2.2713	0.4586	5.6817	1.3657	3.2428	0.2952	0.5468	-0.5224	-0.3036	-0.1695	0.4469	0.218	-0.3225	-0.0775	0.367	0.038	-0.0966	0.2069	-0.0096	0.2732	11.5145	-19.266	-43.4867
8	4.4984	0.2516	0.6993	1.4504	-0.6909	1.6371	0.0751	-0.1572	0.0285	0.1827	0.0756	0.1581	0.1087	-0.1482	-0.1815	0.3425	-0.0417	-0.0089	0.2628	0.0081	0.2994	9.6491	-24.5378	-14.2204
9	5.4228	1.6684	-0.9945	4.0101	1.8548	6.4107	-0.0531	0.0427	-0.0353	0.1996	-0.1509	0.4621	0.0671	-0.3062	0.0992	0.266	0.0426	-0.0326	0.2935	-0.0149	0.3093	30.8054	-19.3553	8.6308
10	1.1478	0.0825	0.3759	0.9793	-0.1508	1.3785	0.0242	-0.1237	-0.0115	0.0655	0.0217	-0.0143	-0.0514	0.1099	-0.0408	0.2487	-0.0224	-0.0029	0.256	-0.0158	0.2182	25.9189	-9.7415	-16.9341
11	4.9056	-1.1338	1.7413	4.9405	-1.5284	5.5037	0.215	0.1423	-0.3525	-0.5077	-0.1099	0.1208	0.3956	0.0508	-0.0566	0.2725	0.0762	-0.052	0.2706	-0.0417	0.2616	-14.693	28.9435	13.1821
12	4.905	-1.9402	-3.006	1.0293	1.4279	3.366	-0.1722	1.1385	-0.8244	-0.2778	-0.4631	0.1676	0.1414	-0.3005	0.5716	0.5643	0.1146	0.1223	0.6179	-0.0429	0.6088	9.4936	30.7813	-6.5836
13	2.3738	-0.466	0.0322	1.7388	-0.7081	1.9162	0.0173	0.0754	-0.0374	-0.3016	-0.1432	-0.1603	0.1207	0.033	0.1158	0.2678	0.1055	0.0031	0.2848	-0.0185	0.28	6.7934	21.6785	15.8123
14	7.3837	0.8779	3.5577	6.3922	2.1399	5.3065	0.4326	0.6582	-0.6917	-0.513	-0.1682	-0.3299	0.8069	0.1261	-0.2708	0.4203	0.0935	0.0437	0.4148	-0.0028	0.386	6.1081	7.3454	16.0086
15	5.516	2.5292	0.5786	4.3557	0.1968	3.7172	0.1149	-0.0208	0.2004	0.0363	-0.0682	0.6211	-0.0498	-0.7581	-0.004	0.4304	-0.111	-0.0592	0.7458	0.0196	0.584	-21.1679	4.5709	27.3906
16	0.76	0.222	-0.5693	1.6835	0.4156	0.4095	0.0446	-0.4366	-0.3193	0.1332	0.0021	0.6505	0.348	-0.7793	0.0605	0.4156	-0.1822	-0.0393	1.1419	0.2467	0.6658	-15.3111	6.9059	54.3531
17	1.7078	0.5129	0.3827	0.7611	-0.0409	2.22	0.147	-0.6501	-0.1752	0.1088	-0.123	0.2223	0.0284	-0.7947	-0.0332	0.2711	-0.0239	-0.0254	0.7822	0.041	0.3713	-9.0355	17.5919	40.2704
18	4.1533	-1.6493	-0.6585	4.7746	-0.4941	0.2953	0.0185	-0.6817	0.0382	0.3085	-0.1314	0.4304	-0.2345	-0.6675	0.069	0.3498	0.1426	-0.0045	0.8623	-0.0728	0.3141	-9.1281	28.7312	41.3959

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 59 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 60 through 96 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 97 through 123 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 124 through 172 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 173 through 293 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 294 through 357 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 358 through 397 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 5 through 123 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 124 through 195 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 196 through 396 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 7 through 96 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 97 through 195 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 196 through 357 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 358 through 397 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 7 through 96 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 97 through 255 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 256 through 357 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 358 through 396 )

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